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Yorodumi- PDB-7o7t: Structure of the PL6 family alginate lyase Patl3640 from Pseudoal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o7t | ||||||
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Title | Structure of the PL6 family alginate lyase Patl3640 from Pseudoalteromonas atlantica T6c in complex with 4-deoxy-L-erythro-5-hexoseulose uronic acid | ||||||
Components | Poly(Beta-D-mannuronate) lyase | ||||||
Keywords | LYASE / beta helix / complex | ||||||
Function / homology | PL-6 family / Chondroitinase B / mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Pectin lyase fold / Pectin lyase fold/virulence factor / 4-deoxy-L-erythro-hex-5-ulosuronic acid / Poly(Beta-D-mannuronate) lyase Function and homology information | ||||||
Biological species | Pseudoalteromonas atlantica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Ballut, L. / Violot, S. / Carrique, L. / Aghajari, N. | ||||||
Citation | Journal: Glycobiology / Year: 2021 Title: Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity. Authors: Violot, S. / Galisson, F. / Carrique, L. / Jugnarain, V. / Conchou, L. / Robert, X. / Thureau, A. / Helbert, W. / Aghajari, N. / Ballut, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o7t.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o7t.ent.gz | 118.6 KB | Display | PDB format |
PDBx/mmJSON format | 7o7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o7t_validation.pdf.gz | 918 KB | Display | wwPDB validaton report |
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Full document | 7o7t_full_validation.pdf.gz | 926.9 KB | Display | |
Data in XML | 7o7t_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 7o7t_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/7o7t ftp://data.pdbj.org/pub/pdb/validation_reports/o7/7o7t | HTTPS FTP |
-Related structure data
Related structure data | 7o77SC 7o78C 7o79C 7o7aC 7o84C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 78820.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas atlantica (strain T6c / ATCC BAA-1087) (bacteria) Strain: T6c / ATCC BAA-1087 / Gene: Patl_3640 / Plasmid: pFO4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q15PP6, mannuronate-specific alginate lyase | ||||||
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#2: Chemical | ChemComp-V4W / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.98 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Mg acetate, 0.1 M Na nitrate, 8% (w/v) PEG 10000, 0.15 mM CYMAL-7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→47.53 Å / Num. obs: 60589 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.99 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.05→2.17 Å / Num. unique obs: 9328 / CC1/2: 0.77 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Patl3640 (PDB ID 7O77) Resolution: 2.05→47.53 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.13 Å2 / Biso mean: 54.6482 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→47.53 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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